It does affect clipnodes, but a clip brush isn't a node itself. See a clipnode as a convex 3D passable block, the player can only walk through clipnodes. By covering complex solid brushes with a clip brush, you prevent them from splitting the rooms clipnode up into many small clipnodes, creating only a few instead.
It's like face splitting, but 3D volume splitting instead. A simpler clipping hull means shorter compile time and faster in-game behaviour, theoretically. The in-game gain is usually not really significant, but since we lack specific profiling tools for HL there's no way to tell.
![:)](http://192.241.182.11/images/smilies/smile.png)
It's one of the reasons I'd recommend to make small detailed brushes func_illusionaries rather than func_walls, or to cover them with clip brushes.